[English] 日本語
Yorodumi
- PDB-5fvm: Cryo electron microscopy of a complex of Tor and Lst8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fvm
TitleCryo electron microscopy of a complex of Tor and Lst8
Components
  • SERINE/THREONINE-PROTEIN KINASE TOR2
  • TARGET OF RAPAMYCIN COMPLEX SUBUNIT LST8MTOR
KeywordsTRANSFERASE / CRYO-EM / TOR / LST8 / MTOR / KINASE / PIKK / S/T PROTEIN KINASE / TORC1 / MTORC1
Function / homology: / :
Function and homology information
Biological speciesKLUYVEROMYCES MARXIANUS (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsBaretic, D. / Berndt, A. / Ohashi, Y. / Johnson, C.M. / Williams, R.L.
CitationJournal: Nat Commun / Year: 2016
Title: Tor forms a dimer through an N-terminal helical solenoid with a complex topology.
Authors: Domagoj Baretić / Alex Berndt / Yohei Ohashi / Christopher M Johnson / Roger L Williams /
Abstract: The target of rapamycin (Tor) is a Ser/Thr protein kinase that regulates a range of anabolic and catabolic processes. Tor is present in two complexes, TORC1 and TORC2, in which the Tor-Lst8 ...The target of rapamycin (Tor) is a Ser/Thr protein kinase that regulates a range of anabolic and catabolic processes. Tor is present in two complexes, TORC1 and TORC2, in which the Tor-Lst8 heterodimer forms a common sub-complex. We have determined the cryo-electron microscopy (EM) structure of Tor bound to Lst8. Two Tor-Lst8 heterodimers assemble further into a dyad-symmetry dimer mediated by Tor-Tor interactions. The first 1,300 residues of Tor form a HEAT repeat-containing α-solenoid with four distinct segments: a highly curved 800-residue N-terminal 'spiral', followed by a 400-residue low-curvature 'bridge' and an extended 'railing' running along the bridge leading to the 'cap' that links to FAT region. This complex topology was verified by domain insertions and offers a new interpretation of the mTORC1 structure. The spiral of one TOR interacts with the bridge of another, which together form a joint platform for the Regulatory Associated Protein of TOR (RAPTOR) regulatory subunit.
History
DepositionFeb 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_image_scans / em_software
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id ..._em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3329
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE TOR2
B: SERINE/THREONINE-PROTEIN KINASE TOR2
C: TARGET OF RAPAMYCIN COMPLEX SUBUNIT LST8
D: TARGET OF RAPAMYCIN COMPLEX SUBUNIT LST8


Theoretical massNumber of molelcules
Total (without water)626,7214
Polymers626,7214
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (-1), (-1), (1) / Vector: 425.6, 425.6)

-
Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE TOR2


Mass: 279407.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLUYVEROMYCES MARXIANUS (yeast) / Gene: KMAR_30040 / Production host: KLUYVEROMYCES MARXIANUS (yeast) / References: UniProt: A0A090BKR7
#2: Protein TARGET OF RAPAMYCIN COMPLEX SUBUNIT LST8 / MTOR


Mass: 33952.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLUYVEROMYCES MARXIANUS (yeast) / Gene: KMAR_20458 / Production host: KLUYVEROMYCES MARXIANUS (yeast) / References: UniProt: A0A090BJK6
Sequence detailsTHE POLYPEPTIDE HAS AN N-TERMINAL 22 RESIDUE TAG AFTER TEV CLEAVGE. IT WAS CLONED FROM GENOMIC DNA. ...THE POLYPEPTIDE HAS AN N-TERMINAL 22 RESIDUE TAG AFTER TEV CLEAVGE. IT WAS CLONED FROM GENOMIC DNA. THE FIRST RESIDUE OF THE CLONED POLYPEPTIDE AFTER THE TAG CORRESPONDS TO RESIDUE 8 OF THE DATABASE ENTRY.

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: COMPLEX OF TOR1 WITH LST8 / Type: COMPLEX
Buffer solutionName: 50 MM HEPES PH 7.4 (23 DEG C), 75 MM KCL, 250 MM NACL, 0.3 % (V/V) CHAPS, 1 MM TCEP
pH: 7.4
Details: 50 MM HEPES PH 7.4 (23 DEG C), 75 MM KCL, 250 MM NACL, 0.3 % (V/V) CHAPS, 1 MM TCEP
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- OTHER, METHOD- 11-13 S AT 4 DEG C,

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: May 16, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 47000 X / Calibrated magnification: 105263 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2RELION3D reconstruction
CTF correctionDetails: EACH PARTICLE (GCTF)
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 6.7 Å / Num. of particles: 28877 / Nominal pixel size: 1.33 Å / Actual pixel size: 1.33 Å
Details: THE FAT AND KINASE DOMAINS (FATKIN) WERE FIT USING 4JSV FATKIN AS AN INITIAL MODEL. THE REMAINDER OF THE STRUCTURE WAS FIT WITH A POLY-ALANINE, AND AN APPROXIMATE SEQUENCE REGISTER WAS ...Details: THE FAT AND KINASE DOMAINS (FATKIN) WERE FIT USING 4JSV FATKIN AS AN INITIAL MODEL. THE REMAINDER OF THE STRUCTURE WAS FIT WITH A POLY-ALANINE, AND AN APPROXIMATE SEQUENCE REGISTER WAS ESTABLISHED BASED ON THE PREDICED HELICAL ELEMENTS IN THE N-TERMINAL REGION AND THE HELICES VISIBLE IN THE EM DENSITY. THE ENTIRE MODEL IS POLY-ALANINE. THE TOPOLOGY OF THE MODEL WAS VERIFIED BY DETERMINING THE STRUCTURES OF VARINTS IN WHICH TENDEM RFPS WERE INSERTED INTO THE STRUCTURE. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3329. (DEPOSITION ID: 14248).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--FLEXIBLE
Atomic model buildingPDB-ID: 4JSV
RefinementHighest resolution: 6.7 Å
Refinement stepCycle: LAST / Highest resolution: 6.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23974 0 0 0 23974

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more